RetrogeneDB ID: retro_rnor_2672

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 9:29431070..29431400(+)
• Located in intron of: ENSRNOG00000012759

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Arl3
• Ensembl ID: ENSRNOG00000019973
• Aliases: None
• Description: ADP-ribosylation factor-like protein 3 [Source:UniProtKB/Swiss-Prot;Acc:P37996]

Sequence

>retro_rnor_2672
GAGAGGAAAATCAGACCATGCTGGAGGAGTTACCTTACAAATATCAATATTCTTCTATTTGTAATCGGCAGTTCAGACAG
AAAAAGGTTTGACGGGTCAAGAACTAATGGAATTACTTGAGGGAGGAAAGTAAGTTGTGTACCAGTATTTGCGTTTGCTA
AGAAGCAGGATCTGTTCACAGCATCACTGGCCTCTGAGACTTCAGAAGGGCTGGACCCATACACCCTCCCGGACCCAGTC
TGGAAGATCCAGTTCTGCTCAGCTATCACAGACAAGGGCCTCCAGGTCGGCACAAACAGGGTCTGCATAAATGTCAGTGT
CAACAAGAAA

Alignment

ORF - retro_rnor_2672 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.57 %
• Parental protein coverage: 61.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QRKIRPYWRSYFENTDILIYVIDSADRKRFEETGQELTELLEEEKLSCVPVLVFANKQDLLTAAPAAEIA
          .RKIRP.WRSY..N..IL..VI.S.DRKRF...G..........K.SCVPV..FA.KQDL.TA..A.E..
Retrocopy ERKIRPCWRSYLTNINILLFVIGSSDRKRFD--GSRTNGIT*GRKVSCVPVFAFAKKQDLFTASLASETS

Parental  EGLNLHTIRDRVWQIQSCSALTGEGVQDGMNWVCKNVNAKKK
          EGL...T..D.VW.IQ.CSA.T..G.Q.G.N.VC.NV...KK
Retrocopy EGLDPYTLPDPVWKIQFCSAITDKGLQVGTNRVCINVSVNKK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	70.46 RPM
SRP017611_kidney	0.00 RPM	28.54 RPM
SRP017611_liver	0.00 RPM	5.58 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2672 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2672 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2672 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017816	1 retrocopy	retro_amel_14,
Rattus norvegicus	ENSRNOG00000019973	1 retrocopy	retro_rnor_2672 ,